Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1112854 | ENA |
REPOSITORIES: ENA
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Project description:Verotoxigenic Escherichia coli (VTEC) are a leading cause of food-borne illness. Fruit and vegetables are recognised as an important source of the pathogen and can account for ~ 25 % of food-borne VTEC outbreaks, globally. The ability of VTEC to colonise leaves and roots of leafy vegetables, spinach (Spinacia oleracea) and lettuce (Lactuca sativa), was compared. The highest levels of colonisation occurred in the roots and rhizosphere, whereas colonisation of the leaves was lower and significantly different between the species. Colonisation of the leaves of prickly lettuce (L. serriola), a wild relative of domesticated lettuce, was especially poor. Differential VTEC gene expression in spinach extracts was markedly different for three tissue types, with little overlap. Comparison of expression in the same tissue type, cell wall polysaccharides, for lettuce and spinach also showed substantial differences, again with virtually no overlap. The transcriptional response was largely dependent on temperatures that are relevant to plant growth, not warm-blooded animals. The data show that VTEC adaptation to plant hosts and subsequent colonisation potential is underpinned by wholescale changes in gene expression that are specific to both plant tissue type and to the species.
2016-08-01 | E-MTAB-3249 | biostudies-arrayexpress
Project description:Verotoxigenic Escherichia coli (VTEC) are a leading cause of food-borne illness. Fruit and vegetables are recognised as an important source of the pathogen and can account for ~ 25 % of food-borne VTEC outbreaks, globally. The ability of VTEC to colonise leaves and roots of leafy vegetables, spinach (Spinacia oleracea) and lettuce (Lactuca sativa), was compared. The highest levels of colonisation occurred in the roots and rhizosphere, whereas colonisation of the leaves was lower and significantly different between the species. Colonisation of the leaves of prickly lettuce (L. serriola), a wild relative of domesticated lettuce, was especially poor. Differential VTEC gene expression in spinach extracts was markedly different for three tissue types, with little overlap. Comparison of expression in the same tissue type, cell wall polysaccharides, for lettuce and spinach also showed substantial differences, again with virtually no overlap. The transcriptional response was largely dependent on temperatures that are relevant to plant growth, not warm-blooded animals. The data show that VTEC adaptation to plant hosts and subsequent colonisation potential is underpinned by wholescale changes in gene expression that are specific to both plant tissue type and to the species.
2016-08-01 | E-MTAB-4120 | biostudies-arrayexpress
Project description:Raw RNAseq data of hydroponically grown crops (cai xin, lettuce, and spinach) subjected under 31 different conditions. Comparative analysis of gene expression across species and stress conditions were carried out.
2024-04-30 | E-MTAB-14018 | biostudies-arrayexpress
Project description:Healthy plants are vital for successful, long-duration missions in space, as they provide the crew with life support, food production, and psychological benefits. The microorganisms that associate with plant tissues play a critical role in improving plant growth, health, and production. To that end, it is necessary to develop methodologies that investigate the metabolic activities of the plant’s microbiome in orbit to enable rapid responses regarding the care of plants in space. In this study, we developed a protocol to characterize the endophytic and epiphytic microbial metatranscriptome of red romaine lettuce, a key salad crop that was grown under International Space Station (ISS)-like conditions. Microbial transcripts enriched from host-microbe total RNA were sequenced using the Oxford Nanopore MinION sequencing platform. Results showed that this enrichment approach was highly reproducible and effective for rapid on-site detection of microbial transcriptional activity. Taxonomic analysis based on 16S and 18S rRNA transcripts identified that the top five most abundant phyla in the lettuce microbiome were Firmicutes, Proteobacteria, Actinobacteria, Bacteroidetes, and Ascomycota. The metatranscriptomic analysis identified the expression of genes involved in many metabolic pathways, including carbohydrate metabolism, energy metabolism, and signal transduction. Network analyses of the expression data show that, within the signal transduction pathway of the fungal community, the Mitogen-Activated Protein Kinase signaling pathway was tightly regulated across all samples and could be a potential driver for fungal proliferation. Our results demonstrated the feasibility of using MinION-based metatranscriptomics of enriched microbial RNA as a method for rapid, on-site monitoring of the transcriptional activity of crop microbiomes, thereby helping to facilitate and maintain plant health for on-orbit space food production.
2021-06-20 | GSE152914 | GEO
Project description:Enzymatic browning on the cut edge of lettuce significantly limits its quality and shelf life. To characterize its molecular mechanisms, we performed comparative transcriptome analysis of three Romaine lettuce cultivars, Parris Island Cos (PC) with low browning potential, Tall Guzmaine (TG) with high degree of browning and Clemente (CL), a medium degree of browning cultivar derived from TG x PC. Before cutting, the phenylpropanoid and oxidative stress genes, such as PAL1, MYB1 and PPO were up-regulated in PC as compared to TG, while the expressions of genes involved in auxin, cytokinin hormone signalings and defense, such as ARF, AHP and PTI in PC were higher than TG. The transcript levels of all these genes in CL were somewhere between TG and PC. On day 3 after cutting when browning was shown up in TG, the expression of these phenylpropanoid and oxidative stress genes were remarkably increased in all three cultivars, even though their levels in TG were still higher than those in PC and CI. In comparison, expressions of the hormone and defense genes were reduced in all three cultivars, but their levels in PC were higher than CI and TG. Exogenous application of IAA and 6-BA inhibited lettuce browning possibly by alleviating the burst of those browning related genes, such as PAL1 and PPO1. These results demonstrate that lettuce tissue browning is controlled by reduced growth hormone (mainly auxin) level and increased phenolics biosynthesis and oxidation. This study provides the useful knowledge and functional markers for lettuce breeders and industry to select low tissue browning cultivar and manage lettuce quality during storage and processing.
2022-12-31 | GSE185049 | GEO
Project description:Lettuce (Lactuca sativa L.) is a highly perishable horticultural crop with a relatively short shelf life due to leaf senescence that limits its commercial value and contributes to food waste. Postharvest senescence varies with influences of both environmental and genetic factors. Preharvest genetic factors can be indicative of postharvest quality. Discovery of additional preharvest markers to assess lettuce shelf life is an important step towards increasing the efficiency of lettuce breeding efforts for improved shelf life. We selected and evaluated three romaine lettuces with variable shelf lives with the aim of identifying preharvest markers of lettuce postharvest shelf life. We evaluated leaf morphological characteristics for each of the three cultivars. To assess molecular indicators of shelf life, we used an RNA sequencing approach to construct transcriptomic profiles of two of the cultivars, a short shelf life (SSL) breeding line 60184 and a long shelf life (LSL) cultivar ‘Okeechobee’ at maturity. We identified 552 upregulated and 315 downregulated differentially expressed (DE) genes between the genotypes. We found that 27 % of the DE lettuce genes had an Arabidopsis thaliana ortholog characterized as senescence-associated, indicating that variable expression of senescence-associated genes (SAGs) could serve as a tool for preharvest markers of postharvest shelf life. Notably, we identified several SAGs and functional groupings with highly differential expression between the cultivars. This includes several jasmonate ZIM-domain (JAZ), jasmonic acid (JA) signaling genes, chlorophyll a-b binding (CAB) chloroplast-associated genes, and cell wall modification genes including pectate lyases (PL) and expansins (EXP). This study presented an innovative approach for identifying molecular markers for preharvest factors linked to postharvest traits for prolonged shelf. These genes could potentially be developed further as preharvest predictors of shelf life for lettuce breeding
2024-02-27 | GSE226302 | GEO